scoresmethods {cocorresp}  R Documentation 
Function to access either species or site scores for specified axes in cocorrespondence analysis ordination methods.
## S3 method for class 'predcoca'
scores(x, choices = c(1, 2),
display = c("sites","species"), ...)
## S3 method for class 'symcoca'
scores(x, choices = c(1, 2),
display = c("sites","species"), scaling = FALSE, ...)
x 
an ordination result 
display 
partial match to access scores for “sites”
“species”, “loadings” or “xmatrix”. The latter
two are only available for 
choices 
numeric; the ordination axes to return. 
scaling 
logical; whether scores should be rescaled
by the quarter root of the eigenvalues using

... 
arguments to be passed to other methods. 
Implements a scores
method for symmetric
cocorrespondence analysis ordination results.
A list with one or more components containing matrices of the requested scores:
species 
A list with two components, 
sites 
A list with two components, 
loadings 
A list with two components, 
xmatrix 
The X matrix. For 
Gavin L. Simpson, based on Matlab code by C.J.F. ter Braak and A.P. Schaffers.
ter Braak, C.J.F and Schaffers, A.P. (2004) CoCorrespondence Analysis: a new ordination method to relate two community compositions. Ecology 85(3), 834–846
scores
, for further details on the method.
## load some data
data(beetles)
data(plants)
## log transform the bettle data
beetles < log(beetles + 1)
## fit the model, a symmetric CoCA
bp.sym < coca(beetles ~ ., data = plants, method = "symmetric")
## extract the scores
scr < scores(bp.sym)
## predictive CoCA using SIMPLS and formula interface
bp.pred < coca(beetles ~ ., data = plants)
scr2 < scores(bp.pred)